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        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.7 (fc7b6b1)

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2019-07-15, 22:25 based on data in: /home/angela/ncbi/ncbi/Data


        General Statistics

        Showing 137/137 rows and 4/5 columns.
        Sample Name% Dups% GCLengthM Seqs
        SRR6398487_1
        93.3%
        55%
        192 bp
        0.8
        SRR6398487_2
        90.2%
        55%
        192 bp
        0.8
        SRR6398488_1
        55.6%
        51%
        220 bp
        0.9
        SRR6398488_2
        53.4%
        51%
        220 bp
        0.9
        SRR6398489_1
        62.9%
        51%
        222 bp
        0.6
        SRR6398489_2
        60.3%
        51%
        222 bp
        0.6
        SRR6398490_1
        50.3%
        46%
        199 bp
        0.4
        SRR6398490_2
        35.6%
        46%
        200 bp
        0.4
        SRR6398491_1
        8.3%
        48%
        224 bp
        0.5
        SRR6398491_2
        7.4%
        48%
        224 bp
        0.5
        SRR6398492_1
        88.4%
        54%
        210 bp
        0.9
        SRR6398492_2
        84.0%
        54%
        210 bp
        0.9
        SRR6398493_1
        75.7%
        52%
        187 bp
        0.8
        SRR6398493_2
        69.3%
        53%
        187 bp
        0.8
        SRR6398494_1
        82.0%
        53%
        210 bp
        0.8
        SRR6398494_2
        79.6%
        53%
        211 bp
        0.8
        SRR6398495_1
        89.5%
        54%
        205 bp
        0.9
        SRR6398495_2
        86.5%
        54%
        206 bp
        0.9
        SRR6398496_1
        28.3%
        43%
        194 bp
        1.0
        SRR6398496_2
        26.2%
        43%
        195 bp
        1.0
        SRR6398497_1
        91.9%
        51%
        214 bp
        0.7
        SRR6398497_2
        89.4%
        51%
        214 bp
        0.7
        SRR6398498_1
        84.6%
        51%
        174 bp
        2.2
        SRR6398498_2
        80.9%
        51%
        173 bp
        2.2
        SRR6398499_1
        35.1%
        49%
        175 bp
        0.7
        SRR6398499_2
        31.6%
        49%
        177 bp
        0.7
        SRR6398500_1
        88.5%
        53%
        166 bp
        1.4
        SRR6398500_2
        84.6%
        53%
        168 bp
        1.4
        SRR6398501_1
        84.9%
        53%
        218 bp
        0.5
        SRR6398501_2
        82.4%
        53%
        219 bp
        0.5
        SRR6398502_1
        87.5%
        53%
        158 bp
        1.5
        SRR6398502_2
        83.2%
        53%
        159 bp
        1.5
        SRR6398503_1
        89.7%
        51%
        206 bp
        0.7
        SRR6398503_2
        86.9%
        51%
        207 bp
        0.7
        SRR6398504_1
        85.6%
        51%
        142 bp
        1.2
        SRR6398504_2
        81.7%
        51%
        143 bp
        1.2
        SRR6398505_1
        16.4%
        38%
        111 bp
        2.0
        SRR6398505_2
        15.5%
        38%
        112 bp
        2.0
        SRR6398506_1
        61.6%
        49%
        136 bp
        1.3
        SRR6398506_2
        59.0%
        49%
        137 bp
        1.3
        SRR6398507_1
        15.6%
        46%
        120 bp
        1.2
        SRR6398507_2
        14.5%
        46%
        121 bp
        1.2
        SRR6398508_1
        20.6%
        47%
        134 bp
        1.2
        SRR6398508_2
        19.1%
        47%
        135 bp
        1.2
        SRR6398509_1
        76.4%
        52%
        214 bp
        0.7
        SRR6398509_2
        73.6%
        52%
        215 bp
        0.7
        SRR6398510_1
        69.2%
        51%
        155 bp
        1.1
        SRR6398510_2
        65.8%
        52%
        155 bp
        1.1
        SRR6398511_1
        91.5%
        51%
        211 bp
        0.9
        SRR6398511_2
        89.2%
        51%
        211 bp
        0.9
        SRR6398512_1
        46.0%
        46%
        147 bp
        0.5
        SRR6398512_2
        43.5%
        46%
        148 bp
        0.5
        SRR6398513_1
        82.7%
        50%
        157 bp
        1.7
        SRR6398513_2
        79.1%
        50%
        158 bp
        1.7
        SRR6398514_1
        15.8%
        45%
        225 bp
        0.6
        SRR6398514_2
        14.6%
        45%
        226 bp
        0.6
        SRR6398515_1
        20.9%
        45%
        206 bp
        0.4
        SRR6398515_2
        18.9%
        45%
        207 bp
        0.4
        SRR6398516_1
        42.0%
        50%
        197 bp
        0.8
        SRR6398516_2
        36.4%
        50%
        198 bp
        0.8
        SRR6398517_1
        29.7%
        49%
        153 bp
        1.8
        SRR6398517_2
        28.0%
        49%
        155 bp
        1.8
        SRR6398518_1
        71.6%
        52%
        210 bp
        0.9
        SRR6398518_2
        68.8%
        52%
        211 bp
        0.9
        SRR6398519_1
        89.7%
        50%
        164 bp
        2.4
        SRR6398519_2
        86.2%
        50%
        164 bp
        2.4
        SRR6398520_1
        86.6%
        48%
        198 bp
        1.0
        SRR6398520_2
        84.1%
        48%
        199 bp
        1.0
        SRR6398521_1
        42.9%
        50%
        189 bp
        0.6
        SRR6398521_2
        41.3%
        50%
        189 bp
        0.6
        SRR6398522_1
        59.5%
        50%
        192 bp
        0.8
        SRR6398522_2
        56.4%
        50%
        193 bp
        0.8
        SRR6398523_1
        80.1%
        51%
        211 bp
        0.6
        SRR6398523_2
        75.8%
        51%
        212 bp
        0.6
        SRR6398524_1
        87.6%
        54%
        203 bp
        0.9
        SRR6398524_2
        85.0%
        54%
        204 bp
        0.9
        SRR6398525_1
        27.0%
        53%
        209 bp
        0.7
        SRR6398525_2
        25.3%
        53%
        210 bp
        0.7
        SRR6398526_1
        91.7%
        54%
        204 bp
        0.7
        SRR6398526_2
        89.0%
        54%
        204 bp
        0.7
        SRR6398527_1
        41.8%
        55%
        193 bp
        1.0
        SRR6398527_2
        40.5%
        55%
        195 bp
        1.0
        SRR6398528_1
        34.3%
        48%
        211 bp
        0.9
        SRR6398528_2
        32.8%
        48%
        211 bp
        0.9
        SRR6398529_1
        77.2%
        55%
        218 bp
        0.9
        SRR6398529_2
        75.1%
        55%
        218 bp
        0.9
        SRR6398530_1
        78.3%
        50%
        208 bp
        0.8
        SRR6398530_2
        71.5%
        50%
        207 bp
        0.8
        SRR6398531_1
        76.0%
        53%
        202 bp
        0.7
        SRR6398531_2
        72.7%
        53%
        202 bp
        0.7
        SRR6398532_1
        57.4%
        52%
        189 bp
        0.8
        SRR6398532_2
        55.1%
        52%
        190 bp
        0.8
        SRR6398533_1
        89.5%
        56%
        224 bp
        0.8
        SRR6398533_2
        83.7%
        56%
        225 bp
        0.8
        SRR6398534_1
        82.2%
        48%
        148 bp
        1.3
        SRR6398534_2
        78.8%
        49%
        149 bp
        1.3
        SRR6398535_1
        36.3%
        47%
        124 bp
        0.6
        SRR6398535_2
        33.4%
        47%
        126 bp
        0.6
        SRR6398536_1
        86.9%
        50%
        217 bp
        0.4
        SRR6398536_2
        83.7%
        50%
        218 bp
        0.4
        SRR6398537_1
        49.5%
        53%
        148 bp
        0.9
        SRR6398537_2
        46.7%
        53%
        150 bp
        0.9
        SRR6398538_1
        47.3%
        52%
        131 bp
        1.1
        SRR6398538_2
        44.8%
        53%
        132 bp
        1.1
        SRR6398539_1
        6.8%
        43%
        132 bp
        0.9
        SRR6398539_2
        6.3%
        43%
        133 bp
        0.9
        SRR6398540_1
        3.0%
        47%
        200 bp
        0.8
        SRR6398540_2
        2.5%
        47%
        202 bp
        0.8
        SRR6398541_1
        85.3%
        55%
        165 bp
        0.8
        SRR6398541_2
        81.4%
        55%
        166 bp
        0.8
        SRR6398542_1
        49.3%
        45%
        152 bp
        0.1
        SRR6398542_2
        46.2%
        44%
        153 bp
        0.1
        SRR6398543_1
        28.6%
        52%
        187 bp
        0.6
        SRR6398543_2
        25.7%
        52%
        188 bp
        0.6
        SRR6398544_1
        13.1%
        49%
        186 bp
        0.4
        SRR6398544_2
        12.0%
        49%
        187 bp
        0.4
        SRR6398545_1
        90.9%
        51%
        207 bp
        0.5
        SRR6398545_2
        87.9%
        51%
        208 bp
        0.5
        SRR6398546_1
        18.3%
        47%
        222 bp
        0.8
        SRR6398547_1
        71.1%
        53%
        189 bp
        0.8
        SRR6398547_2
        69.1%
        53%
        190 bp
        0.8
        SRR6398548_1
        87.9%
        51%
        208 bp
        1.0
        SRR6398548_2
        85.3%
        51%
        208 bp
        1.0
        SRR6398549_1
        17.7%
        48%
        217 bp
        0.6
        SRR6398549_2
        17.0%
        48%
        217 bp
        0.6
        SRR6398550_1
        76.9%
        56%
        212 bp
        1.0
        SRR6398550_2
        72.7%
        56%
        213 bp
        1.0
        SRR6398551_1
        22.9%
        50%
        191 bp
        0.8
        SRR6398551_2
        21.5%
        50%
        192 bp
        0.8
        SRR6398552_1
        69.4%
        56%
        231 bp
        0.8
        SRR6398552_2
        66.9%
        56%
        231 bp
        0.8
        SRR6398553_1
        89.0%
        56%
        224 bp
        0.7
        SRR6398553_2
        85.5%
        56%
        225 bp
        0.7
        SRR6398554_1
        86.9%
        55%
        224 bp
        0.9
        SRR6398554_2
        83.8%
        55%
        225 bp
        0.9
        SRR6398555_1
        62.4%
        55%
        224 bp
        0.6
        SRR6398555_2
        59.7%
        55%
        225 bp
        0.6

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).